parallel_align_seqs_pynast.py

#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division

__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"

import warnings
warnings.filterwarnings('ignore', 'Not using MPI as mpi4py not found')
from qiime.util import (parse_command_line_parameters,
                        get_options_lookup,
                        make_option, 
                        load_qiime_config)
from qiime.align_seqs import pairwise_alignment_methods
from qiime.parallel.align_seqs import ParallelAlignSeqsPyNast

qiime_config = load_qiime_config()
options_lookup = get_options_lookup()

script_info={}
script_info['brief_description']="""Parallel sequence alignment using PyNAST"""
script_info['script_description']="""A wrapper for the align_seqs.py PyNAST option, intended to make use of multicore/multiprocessor environments to perform analyses in parallel."""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Example""","""Align the input file (-i) against using PyNAST and write the output (-o) to $PWD/pynast_aligned_seqs/. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).""","""%prog -i $PWD/inseqs.fasta -o $PWD/pynast_aligned_seqs/"""))
script_info['output_description']="""This results in a multiple sequence alignment (FASTA-formatted)."""

script_info['required_options'] = [\
 options_lookup['fasta_as_primary_input'],\
 options_lookup['output_dir']
]

pairwise_alignment_method_choices = pairwise_alignment_methods.keys()
blast_db_default_help =\
 qiime_config['pynast_template_alignment_blastdb'] or \
 'created on-the-fly from template_alignment'

script_info['optional_options'] = [\
 make_option('-a','--pairwise_alignment_method',\
          type='choice',help='Method to use for pairwise alignments'+\
          ' [default: %default]',\
          default='uclust',choices=pairwise_alignment_method_choices),\
 make_option('-d','--blast_db',type='blast_db',\
          dest='blast_db',help='Database to blast against'+\
          ' [default: %s]' % blast_db_default_help,
          default=qiime_config['pynast_template_alignment_blastdb']),\
    make_option('-e','--min_length',\
          type='int',help='Minimum sequence '+\
          'length to include in alignment [default: 75% of the'+\
          ' median input sequence length]',\
           default=-1),
 make_option('-p','--min_percent_id',action='store',\
          type='float',help='Minimum percent '+\
          'sequence identity to closest blast hit to include sequence in'+\
          ' alignment [default: %default]',default=75.0),\
 options_lookup['jobs_to_start'],
 options_lookup['retain_temp_files'],
 options_lookup['suppress_submit_jobs'],
 options_lookup['poll_directly'],
 options_lookup['cluster_jobs_fp'],
 options_lookup['suppress_polling'],
 options_lookup['job_prefix'],
 options_lookup['seconds_to_sleep']
]

script_info['version'] = __version__

# pynast_template_alignment_fp is required only if it is not 
# provided in qiime_config
if qiime_config['pynast_template_alignment_fp']:
    script_info['optional_options'].append(make_option('-t','--template_fp',\
      type='string',dest='template_fp',help='Filepath for '+\
      'template against [default: %default]',
      default=qiime_config['pynast_template_alignment_fp']))
else:
    script_info['required_options'].append(make_option('-t','--template_fp',\
      type='string',dest='template_fp',\
      help='Filepath for template against',
      default=qiime_config['pynast_template_alignment_fp']))

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    # create dict of command-line options
    params = eval(str(opts))
    
    parallel_runner = ParallelAlignSeqsPyNast(
                                        cluster_jobs_fp=opts.cluster_jobs_fp,
                                        jobs_to_start=opts.jobs_to_start,
                                        retain_temp_files=opts.retain_temp_files,
                                        suppress_polling=opts.suppress_polling,
                                        seconds_to_sleep=opts.seconds_to_sleep)
    parallel_runner(opts.input_fasta_fp,
                    opts.output_dir,
                    params,
                    job_prefix=opts.job_prefix,
                    poll_directly=opts.poll_directly,
                    suppress_submit_jobs=False)


if __name__ == "__main__":
    main()